Plus the automobile loading and unloading process is very labor- and infrastructure-intensive, as anyone who has ridden the AT and observed the operations at Lorton and Sanford has seen.It might be convenient for some, but doing enroute switching would probably have an adverse effect on overall reliability of operations...
Doubt that Amtrak would want to experiment with that....
(And anyway you can drive from Sanford to Jacksonville in less than two hours, so the AT is certainly a viable option to get from the NE to the Jacksonville area with a car.)